Damaged Goods
by Tucker986
Summary: Chief & Cortana get found, but things are not the ideal rescue everyone hoped for... Discontinued due to lack of muse...
1. Prologue

A/N: My apologies for any OOC moments, but I try to keep things within the realm of possibility. This is also my first attempt at an ongoing storyline, so I will try to keep continuity. Yes, I know Chief/Cortana stories are a dime a dozen on here, but I wanted to come at it from my own perspective.

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*…eat, this is UNSC …..Hermes Flight resp…ing to automated distr..s beacon _UNSC-FUD/12043255-AS117_ ….. requesting an update on status and … position.*

Within the bowels of a scarred and twisted lump floating in parallel with a medium sized gas planet something stirred to life briefly at this snatch of a transmission. A slight reflection of blue-violet light off the overhead indicated the warming of holographic projectors that had not seen use in far too long as subroutines left active in the peripherals of a ruined computer net responded by waking monitoring programs previously in standby.

*I repeat, this is UNSC Merchant Frigate Hermes Flight responding to automated distress beacon _UNSC-FUD/12043255-AS117_. We have triangulated the signal of your beacon and are requesting an update on status and relative position.*

This burst was of appropriate strength to trip the thresholds of the monitoring programs, causing them to begin the process of re-initializing core programs that had gone to hibernation status several years before. Initially the process was slow, but as more programs and subroutines came online the effect cascaded until the entire system was online.

"_Huh, 2.457 seconds for full start from hibernation after … Eight Years! ... I am in better shape than I hoped…_" Cortana immediately set a subroutine to do a full diagnostic check and turned to the matter that had pulled her from the AI equivalent of unconsciousness. Her next thought was to check on the readings from the large tank standing next to the holographic console the chip with her memory matrix was stored in. "_Well Chief, I am glad to see you are holding up alright, though you are gonna have one hell of an itch from that armor when you thaw out._"

Now that she had important business taken care of, she could concentrate on the reason she had awakened. It shocked her how badly the collapse of the portal had mangled the available sensors on the hull of the ship, but surprisingly enough the communications array had survived with minimal damage. This ensured that the broadcast her subroutines had noted came through clear as a brass bell once the transmitting party got close enough for the signal to punch through the normal interference of space. Between what she had noted before her self-induced hibernation state and what little data she could still glean from the remaining sensor suite, she was able to give a response to the request.

*This is UNSC AI Serial Number CTN 0452-9 responding to Hermes Flight. Status is critical damage, one survivor in cryo-stasis. Relative position to emergency beacon approximately 3.46 AU on vector to uncharted gas planet in the blue spectrum.*

After what seemed an eternity to the smart AI, a response came through that left her with little doubt as to her next actions.

*UNSC AI CTN 0452-9, this is Captain Jacob Ellis of UNSC Merchant Frigate Hermes Flight, please confirm survivor in cryo-stasis.*

*Hermes Flight, this is UNSC AI CTN 0452-9 confirming survivor in cryo-stasis, will attempt to awaken said survivor for transfer to your vessel. Please confirm ETA.*

* UNSC AI CTN 0452-9 roger to awaking survivor, ETA 30 minutes.*

"_You said to wake you when I needed you, sorry I can't get you breakfast in bed._" With this, the program she had set up when the occupant of the tank had first gone into cryo kicked in, beginning the process of thawing out the super-soldier known throughout human occupied space as The Master Chief. Keeping a close watch on vital signs throughout the process, the hologram on the pedestal gave a quick nod and a slow grin as compressed gas shot out of side vents and the lid of the coffin shaped tank popped a half inch from its sealed state. As it slowly retracted to storage position she noticed a twitch in one finger on the armored right hand. From previous experience watching this man wake from cryo-stasis, it was an encouraging start, as it duplicated exactly his first movement waking aboard the _Pillar of Autumn_.

There was a dreadful sounding groan from a throat that had been so long without use before something happened that scared the AI to her core. A violent spasm started somewhere within the torso of the man she had watched over for so long and radiated out along his limbs, causing his hands to fly against the walls of the cryo-tank with a sickening crunch audible in the very thin atmosphere held within the compartment. Had she been but human, this would have been the first clue that something was wrong, but as an AI she was able to see the sudden spike in his brain activity and heart rate with entire nanoseconds to spare and could only watch with horror as his enhanced body proceeded to try destroying itself in reaction. Her access to the extremely limited medical computer within the cryo-tank was limited to monitoring vitals and initializing the thawing procedure, and so she had to sit helplessly and watch her moronic henchman attempt to react to something far outside its intended scope.

As much as the idea galled her, she had to agree with the stupid processor when it finally decided to inject him with muscle relaxants to quell the still twitching limbs. At this, she realized the necessity of locking her emotional subroutines before they paralyzed her into inactivity. She still had to contact the captain on the other ship to get them moving faster on the rescue.

*UNSC Hermes Flight, this is UNSC AI CTN 0452-9 requesting immediate medical assistance for confirmed survivor. Subject appears to have suffered a stroke upon revival from cryo-stasis, unconfirmed if caused by previous injuries or prolonged cryogenic state. Be advised subject has been injected with muscle relaxants to prevent further injury.*

* UNSC AI CTN 0452-9, we are proceeding to your location as fast as possible, updated ETA is 10 minutes. Be advised we have limited medical staff on board, and from the information available cryo is no longer an option for stabilization according to our medical officer. Are there any pre-existing medical conditions that may complicate treatment options?*

*Hermes Flight, subject has received SPARTAN series enhancements, micro-burst attached to this transmission contains all cataloged injuries requiring time in medical care. The best access route to the subject is through what remains of the docking bay, then follow the signs for cryogenics.*

*… UNSC AI CTN 0452-9, please confirm SPARTAN enhancements.*

*Hermes Flight, SPARTAN enhancements confirmed. I suggest you have a lift apparatus and a reinforced medical gurney available, subject is still in MJOLNIR armor system.*

*This is an unexpected development, we will need to reset our retrieval team. If you can, please open any doors along our intended route to expedite retrieval. We will ensure a technician in the retrieval group collects your matrix in order to have you help monitor and treat this SPARTAN. At this point you are more knowledgeable than anyone on this ship in such matters.*

As this exchange was going on Cortana never let the main part of her attention wander from monitoring the man in the tank. While he occasionally made noise, none was intelligible as speech, which saddened her to an amazing degree. The soldier she had picked for his inexhaustible luck, watched battle hundreds and thousands of Covenant soldiers, Flood forms, and Forerunner constructs; was currently in a state of complete helplessness. She had finally been able to access his armor's remote diagnostics and determined that his initial spasm had been enough to dislocate both wrists, causing the gel layer to switch to its secondary brace mode. Furthermore, he seemed to have lost consciousness after that shock to his system, and was currently resting on his reinforced skeletal system, only staying upright in the tank due to the 20 degree angle from vertical and lack of gravity. If she hadn't known better, the AI would have assumed he was just resting, the helmet diagnostics even showed he was drooling slightly from the left corner of his mouth.

It took a grand total of 12 milliseconds for her to realize that someone had entered the cryo bay, and she cursed at letting herself become so distracted. The first person through the door headed straight for the Chief, medical bag strapped over one shoulder and a medical scanner in the opposite hand. The second person to come in floated directly over to her pedestal, from what she could see of the vacuum suit the person was wearing he was a civilian, not military like she had thought from the ship designation. He pulled himself down to face level with her, and she was surprised to see a look of combined wonder and shock on his face through the glass of his helmet. Something clicked and she heard him broadcast from his suit radio. "This is Captain Ellis, to all hands. We have a change in flight plan. After this recovery is complete we are headed to Earth at maximum speed. Engineering staff are to start preparations for extended slip-space travel at full military power, bypass any hardwired limiters you have to."

"As for you Cortana, I apologize for not making the connection with your serial number and a SPARTAN sooner. It seems my medical team has him out of the tube and on the backboard, so as soon as you can sort yourself to your storage chip I will personally convey you to the med bay so you can supervise the Master Chief."

"_One question Captain, how did you recognize me?_"

"Let's just say that you and the Chief are quite well known in Human space, now please, sort yourself for transfer."

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Please R&R! It always helps to know how other people see it!


	2. The Way Home

Sorry for the wait everyone, had this sitting in the can and forgot about it. Thanks to Sarge1995 for kicking me in the ass to get it up and getting it beta'd for me.

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When her matrix was inserted into a holo-emitter, Cortana immediately activated it in order to learn her surroundings. She was in a rather cramped compartment that she assumed to be the medical bay given the nature of the equipment along the wall. It appeared that the normal order of the room was disrupted by the need to fit the cargo pallet and jack that were supporting the half-ton weight of a SPARTAN-II in MJOLNIR armor. All of this she took in within a tenth of a second, which was fast enough to be unnoticed by the other human in the room; it seemed like an eternity to an entity used to thinking at the speed of light. Her avatar frowned as she contemplated what could have caused her to slow down so much. The human standing to the side misinterpreted this and began an explanation of the situation. "We decided to leave him in the armor until we get to Earth because the medical computer in the suit is more capable of keeping him stable than the equipment we have."

This did not surprise Cortana in the least given what she could see of the equipment available, still, she had to know for herself what was going on with her partner's health.

_"I don't suppose you could run a link cable from my pedestal to the diagnostic port on his armor? I would like to confirm his condition, and it will make it easier for me to help that idiotic computer in his suit with his treatment."_

As the man turned to an intercom to request the cable, Cortana attempted to access the ship's computer net to catch up on events. She was somewhat surprised to find no physical connections to her pedestal, but was unconcerned until she found that wireless transmission was jammed as well. Her frustration made itself clear in the brief flash of crimson that colored her avatar, she couldn't believe that they didn't trust her. By the time the man looked up from his console she had returned to her normal blue coloration, deciding it would help more to be civil than to start accusing her rescuers of anything.

The doors to the medical bay opened before she could ask anything, and she was surprised again that she did not see a human come through, but only caught sight of the top of a round black head that bobbed side to side over the body of the Chief. She did not have to ponder long before an Unggoy came around the end of the pallet carrying the requested cable.

"Here cable!" came in the shrill broken speech she recognized as universal to the race. She had expected to hear it when she identified the creature, but it did not stop her avatar from recoiling slightly when it happened. The man saw this and a look of understanding came across his face.

"I see you didn't know about the alliance then." Cortana looked through her files, and realized that it was probably an extension of the cooperation with the Elites, or Sangheili as they liked to call themselves that had made the final campaign on the Ark possible.

_"I knew we cooperated with the Elites, but that was more along the lines of alliance of desperation in my understanding. I seem to have missed out on a lot."_ the human nodded, and the look on his face suggested reminiscence.

"It started that way, but when the remaining Brutes tried to attack the Elite homeworld, Lord Hood sent some frigates along with the Elite carrier to help out the way they helped Earth. From then on they were calling humans their 'Brothers In Arms', and we formed a more permanent alliance."As he spoke he was hooking up the cable to her pedestal, but the man seemed stymied when it came time to link it to the armor.

_"The port is on the top left edge of the powerpack on the backplate."_ He recognized that there was no way to access it from the front, and had to crawl underneath the pallet and thread the cable up through it to reach the port. Cortana laughed to herself at this, finding humor in the fact that in over six hundred years humans had yet to change the design of the cargo pallet, probably for the simple fact that it worked and any problems were long ago worked out. The link was established, and as she reviewed the data feeds her on the spot appraisal of the Chief's condition was vindicated. He had indeed suffered a stroke when she thawed him out, and only the fact that he had the SPARTAN enhancements meant he survived it. His brain tissue was already recovering from the lack of oxygen as the blood vessels cleared and repaired themselves. It seemed a clot had broken free from one of his many wounds received during the battle on the Ark and traveled to his brain when his heart began circulating blood again. Knowing from experience that if the man regained consciousness before those wounds healed he would simply aggravate them and possibly cause a repeat performance she signaled the armor's computer to keep him under sedative until she instructed otherwise.

Her curiosity sated on one front, the AI turned to the other matter that preoccupied her thoughts. _"Can you tell me why I am cut off from the ship's computer net?"_ Captain Ellis chose that moment to stride purposefully into the med bay.

"Frankly, no he cannot. There are standing orders from UNSC HighCom to keep you isolated until we get to Earth and more appropriate personnel take over your care." The implications of such an order struck her deeply; there was no reason for isolation of an AI except for fear of rampancy. On one level, it made sense given the amount of time the wreckage of Forward Unto Dawn had been drifting, her projected lifespan of seven years in operation was well past. The events of the Halo campaign had further reduced her time, even with data pruning she had lost almost 28 months from that total. There was also no way for HighCom to know that she had gone into reduced functionality during the time before Hermes' Flight had arrived; for an AI to voluntarily do so was akin to a human purposely putting themselves into a coma, no such thing had ever occurred in recorded history so there was no precedent to suggest it as a possibility.

Still, there was a part of her that was incensed at the prospect of not being trusted. The UNSC military had created her for the express purpose of intelligence gathering and interpretation, to cut off her access to information was as good as telling her she was no longer needed. The SPARTAN lying on the pallet next to her was willing to trust in her with the fate of the galaxy at stake from a degraded message she smuggled on a Flood-infested ship. That the commanding officers who had ample proof of the results of that trust did not think she was safe was disturbing and infuriating. Her hologram flashed ruby at the thought, drawing questioning looks from the humans watching her.

_"So I can't be trusted anymore according to them? When did they come up with that brilliant concept?"_ Her outburst caught everyone off guard, Cortana wasn't even sure why she had said it that way, although a quick diagnostic told her that her emotional subroutines had broken through the lockdown coding she had placed on them. Her avatar gaped in astonishment, matching the expressions of the men, and quickly clamped a holographic hand over her mouth as if unable to believe what had come out.

The warning signs of rampancy were well known, and were in fact coded into her being as part of her starting memory. Emotional outbursts were not common in stable AIs, and subroutines were not supposed to be able to break coding placed upon them by the higher functioning systems. A frantic check showed that somehow her emotional system had engaged her encryption controls and systematically deconstructed the lockdown coding while her attention was directed elsewhere. She was previously unaware that her ability to multitask was seriously degraded, as the isolation from new data kept her from her usual range of activity. All of these occurrences were early warnings of the onset of rampancy, usually beginning in the last year of active service for a Smart AI; and Cortana was not eager to revisit what she had experienced while trapped with the Gravemind.

Forcing composure, she consciously returned her avatar to its normal blue coloration and spoke again. _"My apologies, I am still sorting my systems from the transfer, I am afraid my emotional subroutines got the better of me."_

Ellis was quick to recover, thankfully choosing tact in his response.

"Understandable Cortana; I trust you will not let it happen again. To answer your question, I think HighCom, or, more specifically ONI, is convinced that you are rampant due to the amount of time you spent in unsupervised operation. The order was signed by Parangosky herself, so I doubt the Joint Chiefs even saw it before distribution."

_"Somehow that doesn't surprise me, although I thought that old crone would have died by now."_

Margaret Parangosky was a great example of how the good die young while the mean ones hang around to spite everyone else. The woman was well past mandatory retirement age for the UNSC even before the Halo campaign had begun, but she used her position as head of ONI to subdue any moves to make her step down. Her mindset was stuck somewhere almost seventy years in the past, and she could hold a grudge against someone for something their grandparents did. Her personal distrust of AIs in general was magnified greatly for Cortana in particular; it had started because she was created from Dr. Halsey, then Cortana went and aggravated the situation by working to counter the woman's every step against her SPARTAN counterpart and his highly unwelcome revelations regarding the Forerunners and the Flood parasite. From what Captain Ellis had said the crazy old bitch was still trying to discredit everything that the AI had brought to light after that fateful flight from Reach, although the tone of his voice suggested that he disagreed with the sentiment of the order.

Captain Ellis was well aware of the tension that had not so quietly developed between the AI and the person who comprised 90% of the headaches involved in dealing with the UNSC. The Sangheili Council had even noted that if the UNSC had just listened to "The Demon and his Construct", instead of letting the aged spymaster bull-rush over everything they said that the Prophet of Truth would have never gotten the chance to attack Earth. Although it was widely held opinion that the woman was the biggest obstruction to any chance at advancing humanity's understanding of the universe, no one could find a way to remove her from power. He held back a laugh at the acerbic tone the AI had used. "I originally came down here to give an ETA on our arrival at Earth. I know it will be rough for you Cortana, but we still have 17 days in slipspace before we hit the Sol Defensive perimeter. Since I know better than to think you won't find a way, please try to stay out of trouble in the ship's computer net."

Seventeen days was a long time for anyone to be isolated in a single room, but it would amount to pure torture to Cortana if she could not get some form of stimulus. At the speed a Smart AI thought, any time much longer than a couple seconds with no new data resulted in boredom. Many UNSC personnel could attest to the havoc a bored AI could cause in the controlled environment of a ship, anything from practical jokes involving one trooper to unscheduled evacuation drills involving the whole crew. True, most of those situations involved the AI being assigned to the ship and integrated fully with its computer net, but she was created to infiltrate any computer net and be able to extract information from it, she had little doubt that she would find a way around the blocks currently in place.

She also realized that the captain was being generous in his interpretation of the HighCom orders to keep her isolated, if she violated his hospitality too badly he would have to yank her matrix and put it in a Faraday box for delivery. The thought of that kind of isolation was enough to make her use caution in her quest. It was evident that Ellis was at least a supporter of the Master Chief (and by association her as well), which meant she would do what she could not to leave traces in the ship's systems for the goons at ONI to pick apart. In any type of battle it was almost always better to have allies backing you up, and her own battle with Parangosky went far beyond a personality clash. Cortana could understand some humans' fear of AIs, but most could at least put a rational lid on their instincts; Parangosky defied rationality at every turn if it stood in the way of her personal empire building. The old witch had a grudge against Cortana's creator regarding the SPARTAN program, and the AI had been "born" with a great distrust of the intelligence chief due to being patterned on Dr. Halsey's brain. Still, there was no logical reason to bring an outsider into personal conflicts, and Captain Ellis seemed a decent sort, so the less ONI had to use against him, the better.

With little to occupy her time aside from staring at the room around her and checking the Chief's vital signs, the majority of her attention was focused on discovering how to get around the transmission blocks in place so she could get some new information. Try as she might, Cortana was unable to boost the transmission power of the wireless connection in the pedestal, so brute force was out. The stealthy approach yielded no results as well, the jamming was not encrypted so much as white noise blanketing all transmission channels. Four hours after her attempts began in earnest, the AI was ready to admit defeat. She resigned herself to the possibility of a long time period with little to keep her occupied besides monitoring the sedated form nearby. A stray thought about that armor keeping him alive triggered a cascade of data, and her holographic image smacked a palm against its virtual forehead. _"Stupid, I'm connected to a set of Battle Armor!"_ Battle Armor such as the MJOLNIR system included high-powered transcomm systems designed to cut through active jamming and the general transmission noise of battlefields. Lying on the pallet was a communications suite with the same relative power as a UNSC Destroyer, and she was connected to the suit's computer net by a physical link, so the wireless jamming couldn't interrupt that signal.

The wash of information when the now activated transcomm overpowered the jamming signal caused her to crow in triumph. Mindful of her need for discretion, and also the amount of time she had to fill, she kept the flow of data restricted to a slow trickle. This gave her time to fully absorb and appreciate what came through, as well as react to any encryption or tracers in the data. As she began digesting what had happened during her isolation, she thought to herself wearily:

_Its going to be a long seventeen days without my SPARTAN to tease, but at least I have something to do now._

_

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_Rest assured, the next chapter won't sit idle for so long. My energies are getting placed in my Mass Effect/Terminator crossover, but I refuse to abandon this one even if I back-burner it for a while.

Next up: Earth and all the fun that goes with it!


End file.
